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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.8 (d8a0f82)

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2022-06-22, 20:07 based on data in: /home/biocore/kdempsey/elgamal/adoptive_model/fastqc


        General Statistics

        Showing 206/206 rows and 4/5 columns.
        Sample Name% Dups% GCLengthM Seqs
        100_S100_L001_R1_001
        79.6%
        46%
        281 bp
        0.1
        100_S100_L001_R2_001
        70.4%
        45%
        283 bp
        0.1
        101_S101_L001_R1_001
        79.6%
        47%
        280 bp
        0.1
        101_S101_L001_R2_001
        71.3%
        47%
        283 bp
        0.1
        102_S102_L001_R1_001
        81.3%
        44%
        285 bp
        0.1
        102_S102_L001_R2_001
        75.1%
        43%
        287 bp
        0.1
        103_S103_L001_R1_001
        81.2%
        46%
        283 bp
        0.1
        103_S103_L001_R2_001
        72.6%
        46%
        285 bp
        0.1
        10_S10_L001_R1_001
        92.7%
        53%
        301 bp
        0.1
        10_S10_L001_R2_001
        92.4%
        53%
        301 bp
        0.1
        11_S11_L001_R1_001
        92.9%
        53%
        301 bp
        0.1
        11_S11_L001_R2_001
        92.0%
        53%
        301 bp
        0.1
        12_S12_L001_R1_001
        92.6%
        54%
        301 bp
        0.1
        12_S12_L001_R2_001
        91.5%
        53%
        301 bp
        0.1
        13_S13_L001_R1_001
        92.9%
        53%
        301 bp
        0.1
        13_S13_L001_R2_001
        91.6%
        53%
        301 bp
        0.1
        14_S14_L001_R1_001
        92.5%
        53%
        301 bp
        0.1
        14_S14_L001_R2_001
        92.1%
        53%
        301 bp
        0.1
        15_S15_L001_R1_001
        92.5%
        53%
        301 bp
        0.1
        15_S15_L001_R2_001
        92.3%
        53%
        301 bp
        0.1
        16_S16_L001_R1_001
        90.4%
        54%
        301 bp
        0.1
        16_S16_L001_R2_001
        88.2%
        54%
        301 bp
        0.1
        17_S17_L001_R1_001
        93.3%
        53%
        301 bp
        0.1
        17_S17_L001_R2_001
        92.3%
        53%
        301 bp
        0.1
        18_S18_L001_R1_001
        92.2%
        53%
        301 bp
        0.1
        18_S18_L001_R2_001
        92.6%
        53%
        301 bp
        0.1
        19_S19_L001_R1_001
        94.2%
        54%
        301 bp
        0.1
        19_S19_L001_R2_001
        92.6%
        54%
        301 bp
        0.1
        1_S1_L001_R1_001
        92.8%
        52%
        301 bp
        0.1
        1_S1_L001_R2_001
        92.0%
        52%
        301 bp
        0.1
        20_S20_L001_R1_001
        92.6%
        53%
        301 bp
        0.1
        20_S20_L001_R2_001
        92.1%
        53%
        301 bp
        0.1
        21_S21_L001_R1_001
        93.4%
        54%
        301 bp
        0.1
        21_S21_L001_R2_001
        91.8%
        53%
        301 bp
        0.1
        22_S22_L001_R1_001
        92.3%
        54%
        301 bp
        0.1
        22_S22_L001_R2_001
        92.3%
        54%
        301 bp
        0.1
        23_S23_L001_R1_001
        93.0%
        54%
        301 bp
        0.1
        23_S23_L001_R2_001
        92.2%
        53%
        301 bp
        0.1
        24_S24_L001_R1_001
        92.8%
        54%
        301 bp
        0.1
        24_S24_L001_R2_001
        92.0%
        54%
        301 bp
        0.1
        25_S25_L001_R1_001
        93.6%
        54%
        301 bp
        0.2
        25_S25_L001_R2_001
        92.7%
        54%
        301 bp
        0.2
        26_S26_L001_R1_001
        93.4%
        53%
        300 bp
        0.2
        26_S26_L001_R2_001
        93.3%
        53%
        300 bp
        0.2
        27_S27_L001_R1_001
        93.7%
        53%
        301 bp
        0.2
        27_S27_L001_R2_001
        92.3%
        53%
        301 bp
        0.2
        28_S28_L001_R1_001
        93.1%
        53%
        301 bp
        0.2
        28_S28_L001_R2_001
        92.3%
        53%
        301 bp
        0.2
        29_S29_L001_R1_001
        93.9%
        53%
        301 bp
        0.2
        29_S29_L001_R2_001
        92.6%
        54%
        301 bp
        0.2
        2_S2_L001_R1_001
        92.5%
        53%
        301 bp
        0.1
        2_S2_L001_R2_001
        92.0%
        53%
        301 bp
        0.1
        30_S30_L001_R1_001
        92.0%
        53%
        301 bp
        0.1
        30_S30_L001_R2_001
        91.9%
        53%
        301 bp
        0.1
        31_S31_L001_R1_001
        93.3%
        54%
        301 bp
        0.2
        31_S31_L001_R2_001
        92.2%
        54%
        301 bp
        0.2
        32_S32_L001_R1_001
        91.3%
        53%
        301 bp
        0.1
        32_S32_L001_R2_001
        91.1%
        53%
        301 bp
        0.1
        33_S33_L001_R1_001
        92.7%
        54%
        301 bp
        0.2
        33_S33_L001_R2_001
        91.5%
        53%
        301 bp
        0.2
        34_S34_L001_R1_001
        92.4%
        54%
        301 bp
        0.2
        34_S34_L001_R2_001
        92.1%
        54%
        301 bp
        0.2
        35_S35_L001_R1_001
        93.2%
        54%
        301 bp
        0.1
        35_S35_L001_R2_001
        91.5%
        54%
        301 bp
        0.1
        36_S36_L001_R1_001
        92.8%
        53%
        301 bp
        0.1
        36_S36_L001_R2_001
        92.2%
        53%
        301 bp
        0.1
        37_S37_L001_R1_001
        92.9%
        53%
        301 bp
        0.1
        37_S37_L001_R2_001
        91.6%
        53%
        301 bp
        0.1
        38_S38_L001_R1_001
        91.3%
        54%
        301 bp
        0.1
        38_S38_L001_R2_001
        92.0%
        53%
        301 bp
        0.1
        39_S39_L001_R1_001
        93.1%
        53%
        301 bp
        0.1
        39_S39_L001_R2_001
        92.5%
        53%
        301 bp
        0.1
        3_S3_L001_R1_001
        93.8%
        54%
        301 bp
        0.1
        3_S3_L001_R2_001
        92.6%
        53%
        301 bp
        0.1
        40_S40_L001_R1_001
        91.9%
        53%
        301 bp
        0.1
        40_S40_L001_R2_001
        91.8%
        53%
        301 bp
        0.1
        41_S41_L001_R1_001
        92.6%
        53%
        301 bp
        0.2
        41_S41_L001_R2_001
        90.9%
        53%
        301 bp
        0.2
        42_S42_L001_R1_001
        92.1%
        54%
        301 bp
        0.1
        42_S42_L001_R2_001
        91.1%
        54%
        301 bp
        0.1
        43_S43_L001_R1_001
        92.9%
        53%
        301 bp
        0.1
        43_S43_L001_R2_001
        91.0%
        53%
        301 bp
        0.1
        44_S44_L001_R1_001
        92.1%
        54%
        301 bp
        0.1
        44_S44_L001_R2_001
        90.8%
        54%
        301 bp
        0.1
        45_S45_L001_R1_001
        92.7%
        54%
        301 bp
        0.1
        45_S45_L001_R2_001
        90.9%
        54%
        301 bp
        0.1
        46_S46_L001_R1_001
        92.1%
        54%
        301 bp
        0.1
        46_S46_L001_R2_001
        91.2%
        54%
        301 bp
        0.1
        47_S47_L001_R1_001
        92.1%
        54%
        301 bp
        0.1
        47_S47_L001_R2_001
        90.8%
        54%
        301 bp
        0.1
        48_S48_L001_R1_001
        91.7%
        54%
        301 bp
        0.1
        48_S48_L001_R2_001
        90.4%
        54%
        301 bp
        0.1
        49_S49_L001_R1_001
        90.3%
        49%
        290 bp
        0.2
        49_S49_L001_R2_001
        87.3%
        49%
        291 bp
        0.2
        4_S4_L001_R1_001
        93.6%
        52%
        301 bp
        0.1
        4_S4_L001_R2_001
        91.8%
        53%
        301 bp
        0.1
        50_S50_L001_R1_001
        90.4%
        49%
        292 bp
        0.2
        50_S50_L001_R2_001
        87.6%
        49%
        292 bp
        0.2
        51_S51_L001_R1_001
        93.5%
        51%
        296 bp
        0.1
        51_S51_L001_R2_001
        91.0%
        51%
        297 bp
        0.1
        52_S52_L001_R1_001
        92.6%
        50%
        296 bp
        0.1
        52_S52_L001_R2_001
        90.5%
        49%
        297 bp
        0.1
        53_S53_L001_R1_001
        86.1%
        49%
        284 bp
        0.1
        53_S53_L001_R2_001
        81.6%
        49%
        286 bp
        0.1
        54_S54_L001_R1_001
        88.0%
        47%
        286 bp
        0.1
        54_S54_L001_R2_001
        86.3%
        47%
        287 bp
        0.1
        55_S55_L001_R1_001
        86.5%
        48%
        276 bp
        0.1
        55_S55_L001_R2_001
        81.9%
        47%
        278 bp
        0.1
        56_S56_L001_R1_001
        96.2%
        52%
        300 bp
        0.1
        56_S56_L001_R2_001
        93.9%
        52%
        301 bp
        0.1
        57_S57_L001_R1_001
        92.7%
        51%
        297 bp
        0.1
        57_S57_L001_R2_001
        89.1%
        51%
        298 bp
        0.1
        58_S58_L001_R1_001
        85.7%
        46%
        282 bp
        0.1
        58_S58_L001_R2_001
        80.1%
        46%
        284 bp
        0.1
        59_S59_L001_R1_001
        81.4%
        47%
        286 bp
        0.1
        59_S59_L001_R2_001
        72.7%
        46%
        288 bp
        0.1
        5_S5_L001_R1_001
        93.2%
        53%
        301 bp
        0.1
        5_S5_L001_R2_001
        92.1%
        53%
        301 bp
        0.1
        60_S60_L001_R1_001
        85.4%
        47%
        281 bp
        0.1
        60_S60_L001_R2_001
        79.4%
        47%
        283 bp
        0.1
        61_S61_L001_R1_001
        88.0%
        49%
        289 bp
        0.1
        61_S61_L001_R2_001
        82.2%
        49%
        291 bp
        0.1
        62_S62_L001_R1_001
        86.7%
        45%
        285 bp
        0.1
        62_S62_L001_R2_001
        84.0%
        45%
        286 bp
        0.1
        63_S63_L001_R1_001
        83.9%
        46%
        283 bp
        0.1
        63_S63_L001_R2_001
        77.6%
        46%
        285 bp
        0.1
        64_S64_L001_R1_001
        86.7%
        48%
        288 bp
        0.1
        64_S64_L001_R2_001
        82.2%
        48%
        290 bp
        0.1
        65_S65_L001_R1_001
        89.5%
        47%
        288 bp
        0.1
        65_S65_L001_R2_001
        85.3%
        47%
        289 bp
        0.1
        66_S66_L001_R1_001
        84.5%
        46%
        285 bp
        0.1
        66_S66_L001_R2_001
        79.7%
        46%
        287 bp
        0.1
        67_S67_L001_R1_001
        86.4%
        45%
        283 bp
        0.1
        67_S67_L001_R2_001
        80.7%
        45%
        285 bp
        0.1
        68_S68_L001_R1_001
        84.0%
        45%
        279 bp
        0.1
        68_S68_L001_R2_001
        76.4%
        45%
        282 bp
        0.1
        69_S69_L001_R1_001
        81.9%
        47%
        280 bp
        0.1
        69_S69_L001_R2_001
        73.6%
        47%
        284 bp
        0.1
        6_S6_L001_R1_001
        93.5%
        52%
        301 bp
        0.1
        6_S6_L001_R2_001
        92.6%
        53%
        301 bp
        0.1
        70_S70_L001_R1_001
        82.1%
        47%
        282 bp
        0.1
        70_S70_L001_R2_001
        77.0%
        46%
        284 bp
        0.1
        71_S71_L001_R1_001
        81.2%
        45%
        282 bp
        0.1
        71_S71_L001_R2_001
        74.5%
        45%
        285 bp
        0.1
        72_S72_L001_R1_001
        82.6%
        47%
        279 bp
        0.1
        72_S72_L001_R2_001
        75.7%
        47%
        282 bp
        0.1
        73_S73_L001_R1_001
        84.5%
        45%
        278 bp
        0.1
        73_S73_L001_R2_001
        79.9%
        45%
        280 bp
        0.1
        74_S74_L001_R1_001
        73.9%
        46%
        276 bp
        0.1
        74_S74_L001_R2_001
        65.0%
        45%
        278 bp
        0.1
        75_S75_L001_R1_001
        86.1%
        49%
        286 bp
        0.1
        75_S75_L001_R2_001
        80.6%
        48%
        288 bp
        0.1
        76_S76_L001_R1_001
        82.3%
        46%
        281 bp
        0.1
        76_S76_L001_R2_001
        75.6%
        46%
        283 bp
        0.1
        77_S77_L001_R1_001
        81.7%
        47%
        281 bp
        0.1
        77_S77_L001_R2_001
        72.9%
        47%
        284 bp
        0.1
        78_S78_L001_R1_001
        81.9%
        45%
        285 bp
        0.1
        78_S78_L001_R2_001
        77.2%
        45%
        287 bp
        0.1
        79_S79_L001_R1_001
        84.6%
        44%
        285 bp
        0.1
        79_S79_L001_R2_001
        78.9%
        44%
        287 bp
        0.1
        7_S7_L001_R1_001
        93.6%
        52%
        301 bp
        0.1
        7_S7_L001_R2_001
        92.5%
        52%
        301 bp
        0.1
        80_S80_L001_R1_001
        83.1%
        43%
        284 bp
        0.1
        80_S80_L001_R2_001
        77.7%
        43%
        286 bp
        0.1
        81_S81_L001_R1_001
        80.0%
        48%
        283 bp
        0.1
        81_S81_L001_R2_001
        72.0%
        47%
        285 bp
        0.1
        82_S82_L001_R1_001
        83.3%
        49%
        285 bp
        0.1
        82_S82_L001_R2_001
        78.8%
        49%
        287 bp
        0.1
        83_S83_L001_R1_001
        74.5%
        46%
        277 bp
        0.1
        83_S83_L001_R2_001
        61.5%
        46%
        280 bp
        0.1
        84_S84_L001_R1_001
        79.3%
        45%
        283 bp
        0.1
        84_S84_L001_R2_001
        76.0%
        45%
        284 bp
        0.1
        85_S85_L001_R1_001
        82.2%
        48%
        286 bp
        0.1
        85_S85_L001_R2_001
        75.4%
        48%
        288 bp
        0.1
        86_S86_L001_R1_001
        82.9%
        48%
        287 bp
        0.1
        86_S86_L001_R2_001
        79.7%
        48%
        288 bp
        0.1
        87_S87_L001_R1_001
        81.1%
        47%
        279 bp
        0.1
        87_S87_L001_R2_001
        74.3%
        46%
        282 bp
        0.1
        88_S88_L001_R1_001
        83.9%
        43%
        282 bp
        0.1
        88_S88_L001_R2_001
        79.4%
        42%
        284 bp
        0.1
        89_S89_L001_R1_001
        82.6%
        44%
        285 bp
        0.1
        89_S89_L001_R2_001
        76.2%
        44%
        287 bp
        0.1
        8_S8_L001_R1_001
        92.5%
        53%
        301 bp
        0.1
        8_S8_L001_R2_001
        91.5%
        53%
        301 bp
        0.1
        90_S90_L001_R1_001
        81.9%
        47%
        282 bp
        0.1
        90_S90_L001_R2_001
        76.4%
        46%
        284 bp
        0.1
        91_S91_L001_R1_001
        83.9%
        46%
        282 bp
        0.1
        91_S91_L001_R2_001
        75.7%
        46%
        286 bp
        0.1
        92_S92_L001_R1_001
        83.7%
        47%
        280 bp
        0.1
        92_S92_L001_R2_001
        77.0%
        46%
        283 bp
        0.1
        93_S93_L001_R1_001
        78.6%
        47%
        283 bp
        0.1
        93_S93_L001_R2_001
        68.9%
        47%
        286 bp
        0.1
        94_S94_L001_R1_001
        82.3%
        47%
        282 bp
        0.1
        94_S94_L001_R2_001
        77.0%
        46%
        284 bp
        0.1
        95_S95_L001_R1_001
        79.5%
        48%
        273 bp
        0.1
        95_S95_L001_R2_001
        70.8%
        48%
        276 bp
        0.1
        96_S96_L001_R1_001
        80.3%
        47%
        284 bp
        0.1
        96_S96_L001_R2_001
        72.1%
        47%
        286 bp
        0.1
        97_S97_L001_R1_001
        77.3%
        47%
        283 bp
        0.1
        97_S97_L001_R2_001
        67.9%
        47%
        285 bp
        0.1
        98_S98_L001_R1_001
        84.6%
        44%
        284 bp
        0.1
        98_S98_L001_R2_001
        78.8%
        44%
        286 bp
        0.1
        99_S99_L001_R1_001
        84.0%
        44%
        280 bp
        0.1
        99_S99_L001_R2_001
        77.0%
        44%
        282 bp
        0.1
        9_S9_L001_R1_001
        92.9%
        53%
        301 bp
        0.1
        9_S9_L001_R2_001
        92.2%
        53%
        301 bp
        0.1

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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